Handle arrays in the cache of the model by using the memoization library. Speeds up the single model case too.

cara/models.py

@@ -31,10 +31,16 @@ the same for all parameters of a single model.
 
 """
 from dataclasses import dataclass
-import functools
 import numpy as np
 import typing
 
+if not typing.TYPE_CHECKING:
+    from memoization import cached
+else:
+    # Workaround issue https://github.com/lonelyenvoy/python-memoization/issues/18
+    # by providing a no-op cache decorator when type-checking.
+    cached = lambda *cached_args, **cached_kwargs: lambda function: function  # noqa
+
 from .dataclass_utils import nested_replace
 
 
@@ -593,7 +599,7 @@ class InfectedPopulation(Population):
 
         return self.emission_rate_when_present()
 
-    @functools.lru_cache()
+    @cached()
     def emission_rate(self, time) -> float:
         """
         The emission rate of the entire population.
@@ -622,7 +628,7 @@ class ConcentrationModel:
 
         return k + self.virus.decay_constant + self.ventilation.air_exchange(self.room, time)
 
-    @functools.lru_cache()
+    @cached()
     def state_change_times(self):
         """
         All time dependent entities on this model must provide information about
@@ -645,8 +651,11 @@ class ConcentrationModel:
                 return change_time
         return 0
 
-    @functools.lru_cache()
+    @cached()
     def concentration(self, time: float) -> float:
+        # Note that time is not vectorised. You can only pass a single float
+        # to this method.
+
         if time == 0:
             return 0.0
         IVRR = self.infectious_virus_removal_rate(time)

cara/tests/apps/calculator/test_report_generator.py

@@ -1,3 +1,5 @@
+import time
+
 import pytest
 
 from cara.apps.calculator import model_generator
@@ -15,10 +17,18 @@ def baseline_form(baseline_form_data):
 
 
 def test_generate_report(baseline_form):
-    model = baseline_form.build_model()
+    # This is a simple test that confirms that given a model, we can actually
+    # generate a report for it. Because this is what happens in the cara
+    # calculator, we confirm that the generation happens within a reasonable
+    # time threshold.
+    time_limit: float = 1.5  # seconds
 
+    start = time.perf_counter()
+    model = baseline_form.build_model()
     report = report_generator.build_report("", model, baseline_form)
+    end = time.perf_counter()
     assert report != ""
+    assert end - start < time_limit
 
 
 @pytest.mark.parametrize(

requirements.txt

@@ -37,6 +37,7 @@ jupyterlab-widgets==1.0.0
 kiwisolver==1.3.1
 MarkupSafe==1.1.1
 matplotlib==3.3.4
+memoization==0.3.2
 mistune==0.8.4
 nbclient==0.5.2
 nbconvert==6.0.7

setup.py

@@ -22,6 +22,7 @@ REQUIREMENTS: dict = {
         'ipywidgets',
         'Jinja2',
         'matplotlib',
+        'memoization',
         'mistune',
         'numpy',
         'qrcode[pil]',